I am having a bit hard issue to describe so bear with me. Refer to image below.

1. I have an animated can that has been animated using deformations. It has a transform effector "A" with linear falloff to animate stretch and squash as well as a transform effector "B" to transform deformed mesh. I used this tutorial to animate mesh in whole: http://www.youtube.com/watch?v=ofMj-W0-hhE
2. Now comes the part that is hard to describe. After animating any rotation with the transform effector B such as ~-130° in z-axis the lightning does not seem to follow. As if the mesh stayed in position and the lightning is calculated to that. Lights have no animation at all, just the transform effector "B". Please refer to image to get better idea.

This is my first ever 3D test with modo and I cannot understand what is going wrong. Thank you for your help!

Sounds kind of funky...
I have only seen something remotely like it in OpenGL view when I have a spotlight on a plane - then resize the plane and the light cone intersection with the plane will seemingly be stretched accordingly (but only in OpenGL view - while the Preview render window shows the light cone correctly as unchanged). Then doing a "Freeze > Scale" puts things right in the OpenGL view again.

However the problem you observe, seems more complex, so I would recommend you to submit a bug-report with the Foundry.

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